* {{App|[[Wikipedia:Maxima (software)|Maxima]]|A [[Wikipedia:Maple (software)|Maple]]/[[Wikipedia:Wolfram Mathematica|Mathematica]]-like program with a wxWidgets based frontend.|http://maxima.sourceforge.net/|{{Pkg|maxima}} {{Pkg|wxmaxima}}}}

+

* {{App|[[Wikipedia:Mathomatic|Mathomatic]]|General purpose Computer Algebra System written in C.|http://www.mathomatic.org/|{{Pkg|mathomatic}}}}

−

* {{App|[[Wikipedia:PARI/GP|PARI/GP]]|A computer algebra system designed for fast computations in number theory.|http://pari.math.u-bordeaux.fr/|{{Pkg|pari}}}}

+

* {{App|[[Wikipedia:Maxima (software)|Maxima]]|[[Wikipedia:Maple (software)|Maple]]/[[Wikipedia:Wolfram Mathematica|Mathematica]]-like program with a wxWidgets based frontend.|http://maxima.sourceforge.net/|{{Pkg|maxima}} {{Pkg|wxmaxima}}}}

−

* {{App|[[Sage]]|A algebra system similar to Maxima, but written in Python.|http://www.sagemath.org/|{{Pkg|sage-mathematics}}}}

+

* {{App|[[Wikipedia:PARI/GP|PARI/GP]]|Computer algebra system designed for fast computations in number theory.|http://pari.math.u-bordeaux.fr/|{{Pkg|pari}}}}

* {{App|EngLab|A cross-compile mathematical platform with a C like syntax.|http://englab.bugfest.net|{{AUR|englab}}}}

+

* {{App|EngLab|Cross-compile mathematical platform with a C like syntax.|http://englab.bugfest.net|{{AUR|englab}}}}

−

* {{App|[[Wikipedia:Euler (software)|Euler]]|A numerical application designed for higher level math such as calculus, optimization, and statistics that uses Maxima for symbolic operations.|http://euler.sourceforge.net|{{AUR|euler}}}}

+

* {{App|[[Wikipedia:Euler (software)|Euler]]|Numerical application designed for higher level math such as calculus, optimization, and statistics that uses Maxima for symbolic operations.|http://euler.sourceforge.net|{{AUR|euler}}}}

−

* {{App|[[Wikipedia:FreeMat|FreeMat]]|A Matlab-like program that supports many of its functions and features a codeless interface to external C, C++, and Fortran code, further parallel distributed algorithm development (via MPI), and 3D visualization capabilities.|http://freemat.sourceforge.net/|{{Pkg|freemat}}}}

+

* {{App|[[Wikipedia:FreeMat|FreeMat]]|Matlab-like program that supports many of its functions and features a codeless interface to external C, C++, and Fortran code, further parallel distributed algorithm development (via MPI), and 3D visualization capabilities.|http://freemat.sourceforge.net/|{{Pkg|freemat}}}}

* {{App|[[Wikipedia:Scilab|Scilab]]|A Matlab alternative used for numerical computations, its syntax is not equivalent to that of Matlab, but it can be easily converted.|http://www.scilab.org/|{{AUR|scilab}}}}

+

* {{App|[[Sage]]|Mathematics software system, that combines many existing open-source packages into a common Python interface. Alternative to Magma, Maple, Mathematica and Matlab.|http://www.sagemath.org|{{Pkg|sage-mathematics}}}}

+

* {{App|[[Wikipedia:Scilab|Scilab]]|Matlab alternative used for numerical computations. Its syntax is not equivalent to that of Matlab, but it can be easily converted.|http://www.scilab.org/|{{AUR|scilab}}}}

* {{App|[[Wikipedia:QtiPlot|QtiPlot]]|A platform-independent application used for interactive scientific graphing and data analysis, similar to the proprietary [[Wikipedia: Origin (software)|Origin]] or [[Wikipedia:SigmaPlot|SigmaPlot]].|http://soft.proindependent.com/qtiplot.html|{{Pkg|qtiplot}}}}

+

* {{App|[[Wikipedia:QtiPlot|QtiPlot]]|Platform-independent application used for interactive scientific graphing and data analysis, similar to the proprietary [[Wikipedia: Origin (software)|Origin]] or [[Wikipedia:SigmaPlot|SigmaPlot]].|http://soft.proindependent.com/qtiplot.html|{{Pkg|qtiplot}}}}

−

* {{App|[[Wikipedia:ROOT|ROOT]]|A data analysis program and library (originally for particle physics) developed by CERN.|http://root.cern.ch/drupal/|{{AUR|root}}}}

+

* {{App|[[Wikipedia:ROOT|ROOT]]|Data analysis program and library (originally for particle physics) developed by CERN.|http://root.cern.ch/drupal/|{{AUR|root}}}}

−

* {{App|[[Wikipedia:SciDAVis|SciDAVis]]|A fork of QtiPlot with the goal of being better documented and more user friendly.|http://scidavis.sourceforge.net/|{{AUR|scidavis}}}}

+

* {{App|[[Wikipedia:SciDAVis|SciDAVis]]|Fork of QtiPlot with the goal of being better documented and more user friendly.|http://scidavis.sourceforge.net/|{{AUR|scidavis}}}}

See also [[List of Applications#Spreadsheets]]

See also [[List of Applications#Spreadsheets]]

−

=== Chemistry and Biology ===

+

=== Chemistry and biology ===

−

====Computational Biology and Bioinformatics====

+

+

====Computational biology and bioinformatics====

+

{{Wikipedia|List of open source bioinformatics software}}

{{Wikipedia|List of open source bioinformatics software}}

−

* {{App|[[Wikipedia:BALL|BALL]] (Biochemical Algorithms Library)|An application framework in C++ that provides an extensive set of data structures as well as classes for molecular nechanics, advanced solvation methods, comparison and analysis of protein structures, file import/export, and visualization.|http://www.ball-project.org/|{{AUR|ball}}}}

+

* {{App|[[Wikipedia:BALL|BALL]] (Biochemical Algorithms Library)|Application framework in C++ that provides an extensive set of data structures as well as classes for molecular nechanics, advanced solvation methods, comparison and analysis of protein structures, file import/export, and visualization.|http://www.ball-project.org/|{{AUR|ball}}}}

−

* {{App|[[Wikipedia:BioJava|BioJava]]|A set of Java tools for computational biology, as well as bioinformatics.|http://biojava.org/wiki/Main_Page|{{AUR|biojava}}}}

+

* {{App|[[Wikipedia:BioJava|BioJava]]|Set of Java tools for computational biology, as well as bioinformatics.|http://biojava.org/wiki/Main_Page|{{AUR|biojava}}}}

−

* {{App|[[Wikipedia:Biopython|Biopython]]|A Python package with tools for computational biology, as well as bioinformatics.|http://biopython.org/wiki/Biopython|{{AUR|python-biopython}} {{AUR|python2-biopython}}}}

+

* {{App|[[Wikipedia:Biopython|Biopython]]|Python package with tools for computational biology, as well as bioinformatics.|http://biopython.org/wiki/Biopython|{{AUR|python-biopython}} {{AUR|python2-biopython}}}}

−

* {{App|[[Wikipedia:EMBOSS|EMBOSS]] (European Molecular Biology Open Software Suite)|An open source software analysis package specially developed for the needs of the molecular biology and bioinformatics user community.|http://emboss.sourceforge.net/|{{AUR|emboss}}}}

* {{App|[[Wikipedia:PyMOL|PyMOL]]|An open-source molecular visualization system that can produce high quality 3D images of small molecules and biological macromolecules, such as proteins.|http://pymol.org|{{AUR|pymol}}}}

+

* {{App|[[Wikipedia:PyMOL|PyMOL]]|Open-source molecular visualization system that can produce high quality 3D images of small molecules and biological macromolecules, such as proteins.|http://pymol.org|{{AUR|pymol}}}}

−

* {{App|[[Wikipedia:RasMol|RasMol]]|A computer program written for molecular graphics visualization intended and used primarily for the depiction and exploration of biological macromolecule structures.|http://www.rasmol.org/|{{AUR|rasmol}}}}

+

* {{App|[[Wikipedia:RasMol|RasMol]]|Computer program written for molecular graphics visualization intended and used primarily for the depiction and exploration of biological macromolecule structures.|http://www.rasmol.org/|{{AUR|rasmol}}}}

* {{App|[[Wikipedia:Quantum ESPRESSO|Quantum ESPRESSO]]|An integrated suite of applications for electronic-structure calculations and materials modeling at nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials (both norm-conserving and ultrasoft).|http://www.quantum-espresso.org/|{{AUR|quantum-espresso}}}}

* {{App|[[Wikipedia:Quantum ESPRESSO|Quantum ESPRESSO]]|Integrated suite of applications for electronic-structure calculations and materials modeling at nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials (both norm-conserving and ultrasoft).|http://www.quantum-espresso.org/|{{AUR|quantum-espresso}}}}

==== Image manipulation ====

==== Image manipulation ====

−

* {{App|[[Wikipedia:ImageJ|ImageJ]]|A Java-based image processing and analysing program that provides extensibility via plugins and macros. It is widely used in microscopy (e.g. for cell counting).|http://rsb.info.nih.gov/ij|{{AUR|imagej}}}}

+

+

* {{App|[[Wikipedia:ImageJ|ImageJ]]|Java-based image processing and analysing program that provides extensibility via plugins and macros. It is widely used in microscopy (e.g. for cell counting).|http://rsb.info.nih.gov/ij|{{AUR|imagej}}}}

* {{App|[[Wikipedia:Celestia|Celestia]]|A 3D astronomy simulation program that allows users to travel through an extensive universe, modeled after reality, at any speed, in any direction and at any time in history.|http://www.shatters.net/celestia/|{{Pkg|celestia}}}}

+

* {{App|[[Wikipedia:Celestia|Celestia]]|3D astronomy simulation program that allows users to travel through an extensive universe, modeled after reality, at any speed, in any direction and at any time in history.|http://www.shatters.net/celestia/|{{Pkg|celestia}}}}

* {{App|GoQat|A camera acquisition software, especially for QSI cameras, that provides other features such as autoguiding, focusing help and others.|http://canburytech.net/GoQat/|{{AUR|goqat}}}}

+

* {{App|GoQat|Camera acquisition software, especially for QSI cameras, that provides other features such as autoguiding, focusing help and others.|http://canburytech.net/GoQat/|{{AUR|goqat}}}}

−

* {{App|[[Wikipedia:KStars|KStars]]|A planetarium application that provides an accurate graphical simulation of the night sky, from any location on Earth, at any date and time. It is included in KDE Edu.|http://edu.kde.org/kstars/|{{Pkg|kdeedu-kstars}}}}

+

* {{App|[[Wikipedia:KStars|KStars]]|Planetarium application that provides an accurate graphical simulation of the night sky, from any location on Earth, at any date and time. It is included in KDE Edu.|http://edu.kde.org/kstars/|{{Pkg|kdeedu-kstars}}}}

−

* {{App|Open PHD Guiding|A telescope autoguiding software based on the famous PHD Guiding.|http://code.google.com/p/open-phd-guiding/|{{AUR|open-phd-guiding}}}}

+

* {{App|Open PHD Guiding|Telescope autoguiding software based on the famous PHD Guiding.|http://code.google.com/p/open-phd-guiding/|{{AUR|open-phd-guiding-svn}}}}

* {{App|[[Wikipedia:Cartes du Ciel|Skychart / Cartes du Ciel]]|A planetarium that maps out and labels most of the constellations, planets, and objects you can see with a telescope. It can also download Digitized Sky Survey Charts and superimpose images over these charts.|http://www.ap-i.net/skychart/start/|{{AUR|skychart}}}}

+

* {{App|[[Wikipedia:Cartes du Ciel|Skychart / Cartes du Ciel]]|Planetarium that maps out and labels most of the constellations, planets, and objects you can see with a telescope. It can also download Digitized Sky Survey Charts and superimpose images over these charts.|http://www.ap-i.net/skychart/start/|{{AUR|skychart}}}}

* {{App|[[gEDA]]|A full suite and toolkit of Electronic Design Automation tools that are used for electrical circuit design, schematic capture, simulation, prototyping, and production.|http://www.geda-project.org/|{{Pkg|geda-gaf}}}}

+

* {{App|[[gEDA]]|Full suite and toolkit of Electronic Design Automation tools that are used for electrical circuit design, schematic capture, simulation, prototyping, and production.|http://www.geda-project.org/|{{Pkg|geda-gaf}}}}

−

* {{App|[[Wikipedia:KiCAD|KiCAD]]|A software suite for electronic design automation (EDA) that facilitates the design of schematics for electronic circuits and their conversion to PCB (printed circuit board).|http://www.kicad-pcb.org/display/KICAD/KiCad+EDA+Software+Suite|{{Pkg|kicad}}}}

+

* {{App|[[Wikipedia:KiCAD|KiCAD]]|Software suite for electronic design automation (EDA) that facilitates the design of schematics for electronic circuits and their conversion to PCB (printed circuit board).|http://www.kicad-pcb.org/display/KICAD/KiCad+EDA+Software+Suite|{{Pkg|kicad}}}}

−

* {{App|KLogic|An application used for easily building and simulating digital circuits.|http://www.a-rostin.de/|{{AUR|klogic}}}}

+

* {{App|KLogic|Application used for easily building and simulating digital circuits.|http://www.a-rostin.de/|{{AUR|klogic}}}}

−

* {{App|[[Wikipedia:KTechLab|KTechLab]]|An IDE for electronic and PIC microcontroller circuit design and simulation featuring an extensive circuit designer with autorouting and simulation of all common electronic components and logic elements.|http://sourceforge.net/projects/ktechlab/|{{Pkg|ktechlab}}}}

+

* {{App|[[Wikipedia:KTechLab|KTechLab]]|IDE for electronic and PIC microcontroller circuit design and simulation featuring an extensive circuit designer with autorouting and simulation of all common electronic components and logic elements.|http://sourceforge.net/projects/ktechlab/|{{Pkg|ktechlab}}}}

* {{App|[[Wikipedia:Quite Universal Circuit Simulator|Qucs]]|An electronics circuit simulator application that gives you the ability to set up a circuit with a graphical user interface and simulate its large-signal, small-signal and noise behaviour.|http://qucs.sourceforge.net/|{{Pkg|qucs}}}}

+

* {{App|[[Wikipedia:Quite Universal Circuit Simulator|Qucs]]|Electronics circuit simulator application that gives you the ability to set up a circuit with a graphical user interface and simulate its large-signal, small-signal and noise behaviour.|http://qucs.sourceforge.net/|{{Pkg|qucs}}}}

* {{App|[[Wikipedia:Step (software)|Step]]|A two-dimensional physics simulation engine that is included in the KDE desktop as part of KDE Edu.|http://edu.kde.org/step/|{{Pkg|kdeedu-step}}}}

−

==== Unit Conversion ====

+

* {{App|ConvertAll|Unit conversion application that allows one to combine units in any way (e.g. inches per decade), even if it does not make sense.|http://convertall.bellz.org/|{{AUR|convertall}}}}

−

* {{App|ConvertAll|A unit conversion application that allows one to combine units in any way (e.g. inches per decade), even if it does not make sense.|http://convertall.bellz.org/|{{AUR|convertall}}}}

+

* {{App|Gonvert|Conversion utility that allows conversion between many units like CGS, Ancient, Imperial with many categories like length, mass, numbers, etc.|http://www.unihedron.com/projects/gonvert/|{{AUR|gonvert}}}}

−

* {{App|Gonvert|A conversion utility that allows conversion between many units like CGS, Ancient, Imperial with many categories like length, mass, numbers, etc.|http://www.unihedron.com/projects/gonvert/|{{AUR|gonvert}}}}

+

* {{App|[[Wikipedia:GNU Units|Units]]|Command-line unit converter and calculator that can handle multiplicative scale changes, nonlinear conversions such as Fahrenheit to Celsius or wire gauge and others.|http://www.gnu.org/s/units/|{{Pkg|units}}}}

−

* {{App|[[Wikipedia:GNU Units|Units]]|A command-line unit converter and calculator that can handle multiplicative scale changes, nonlinear conversions such as Fahrenheit to Celsius or wire gauge and others.|http://www.gnu.org/s/units/|{{Pkg|units}}}}

Computer algebra system

Fermat — Computer algebra system that does arithmetic of arbitrarily long integers and fractions, multivariate polynomials, symbolic calculations, matrices over polynomial rings, graphics, and other numerical calculations.

FreeMat — Matlab-like program that supports many of its functions and features a codeless interface to external C, C++, and Fortran code, further parallel distributed algorithm development (via MPI), and 3D visualization capabilities.

Chemistry and biology

Computational biology and bioinformatics

BALL (Biochemical Algorithms Library) — Application framework in C++ that provides an extensive set of data structures as well as classes for molecular nechanics, advanced solvation methods, comparison and analysis of protein structures, file import/export, and visualization.

Quantum ESPRESSO — Integrated suite of applications for electronic-structure calculations and materials modeling at nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials (both norm-conserving and ultrasoft).

Skychart / Cartes du Ciel — Planetarium that maps out and labels most of the constellations, planets, and objects you can see with a telescope. It can also download Digitized Sky Survey Charts and superimpose images over these charts.

KTechLab — IDE for electronic and PIC microcontroller circuit design and simulation featuring an extensive circuit designer with autorouting and simulation of all common electronic components and logic elements.